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United States Department of Agriculture

Agricultural Research Service


Location: Crops Pathology and Genetics Research

2009 Annual Report

1a. Objectives (from AD-416)
1. Develop sustainable disease control practices for grapevines. 2. Develop sustainable vineyard floor management practices. 3. Develop sustainable water management practices for vineyards. 4. Investigate the impacts of vineyard practices on soil microbial ecology. 5. Identify & characterize viral & graft-transmissable agents of grapevine.

1b. Approach (from AD-416)
1. Characterize the infection process of grapevine roots by the fungal pathogen Armillaria mellea, the causal agent of Armillaria root disease; Characterize the significance of riparian areas in the spread of Pierce's disease; and Identify and characterize viral and graft transmissible agents. 2. Identify differences in regional populations of Conyza canadensis, cover crops that effectively compete with c. canadensis, and effects of soil resource availability on competition between cover crops and C. canadensis; and Identify cover crops that effectively compete with problematic weeds. 3. Evaluate the interactive effects of irrigation practices and vineyard floor management practices on grapevine yield, growth, physiology, and nutrition. 4. Examine the effect of cover crop functional type on soil microbial communities and microbially-mediated soil processes; Characterize rhizosphere communities associated with Vitis rootstocks; and Examine the impacts of vineyard floor practices on mycorrhizae. REPLACING 5306-21220-003-00D (01/07)

3. Progress Report
In FY09, we initiated field and laboratory trials to identify sustainable control methods for trunk pathogens of grape. The causal fungi (Botryosphaeria, Eutypa, Phaeoacremonium, Phaeomoniella) are so-named because they decompose the woody trunk of the grapevine. The full economic impact of two such trunk pathogens (Eutypa, Botryosphaeria) amounts to a net income loss of $260M annually for winegrapes in CA. This figure does not include losses suffered by CA raisin and table grape producers (31% and 10% of CA grape production, respectively) or grape producers outside of CA. The serious losses that the grape industry experiences from trunk diseases, the spread of trunk pathogens to nacent grape growing regions outside CA, and the loss of a key fungicide for trunk disease control (benomyl) was emphasized by stakeholders to scientists in the project in FY08. Our goal is to develop control recommendations for eastern and western US vineyards that are not focused on fungicide use. Deliverables of the research, to be completed in FY12, are preventative pruning practices and disease resistant grape varieties for US grape growers. In FY09, we used deep sequencing technology to identify viruses causing necrotic union disorders of grape, with the goal of developing diagnostic tools to aid in clean plant material programs across the US. Necrotic union disorders, like other viruses, cause a range of problems, including nutrient deficiencies and yield losses. They are only controlled by propagating virus-free plants. Preliminary results identified no known viruses. Thus, a novel virus is likely involved, and its characterization is in progress. In FY09, we continued a field trial established in FY08, to identify vineyard floor management practices that control weeds. Preliminary results show that infestations of certain weeds (e.g., panicle willowherb) are exacerbated when the soil is not tilled, and that others are minimized by tillage (e.g., California burclover). In addition to the focus on weeds, we also monitor grapevine nutrition and yield, grape juice properties (titratable acidity, soluble solids, pH), and soil moisture, as growers are concerned about possible negative effects of vineyard floor management practices on these aspects of grape production. In FY09, we continued a field trial established in FY06, to identify soil microbes that are specific to individual grapevine rootstocks. Preliminary results show that there are some groups of soil microbes shared in common among all rootstocks, which make up the general grapevine soil microbial community. Microbes associated with individual rootstocks were identified based on C-substrate use and DNA-based methods. We also analysis of nematode communities, and their response to various vineyard floor management practices, specifically cover cropping and weed control.

4. Accomplishments
1. Rapid and reliable infection assay for Armillaria root disease. Armillaria root disease is a problem in vineyards established on land previously occupied by oak forests. Our goal is to identify Armillaria-resistant rootstocks that grapevines can be grafted onto before planting them in infected soil because there are no economically viable means of ridding the soil of the pathogen, and there are no fungicides to cure an infected vine. ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA developed an infection assay for the causal pathogen, Armillaria mellea, in order to rapidly infect plants in the laboratory and measure levels of infection in the roots starting 2 weeks after inoculation. This infection assay is an improvement on a previous assay that brought about infection in 7-18 months, and will greatly advance screening commercial and experimental rootstocks, in order to identify those that are Armillaria-resistant.

2. Use of grape rootstocks as indicator plants to identify the presence of viruses. Grapevine viruses causing necrotic union and stem necrosis distortion are difficult to distinguish from other pathogens because they are difficult to detect and because symptoms do not appear for 3-6 years after infection. ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA established a field trial to identify rootstocks that, when virus-infected material is grafted onto them, develop symptoms in only 2 years and thus serve as indicators of the virus. Two rootstocks will now serve as indicators for the viruses. These rootstocks will lead to the development of diagnostic molecular and/or serological probes to recognize the virus in clean plant material programs that propagate grapevines for nurseries and vineyards across the US.

3. Cover crops increase the availability of soil nitrogen (N) for grapes and improve yields. Cover crops are becoming increasingly popular in vineyards as a means of minimizing soil erosion, but little is known about their potential positive effects on grapevine nutrition or their possible negative effects on greenhouse gas emissions (i.e., nitrous oxide). In a field trial, ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA demonstrated that cover crops Triticale and rye prevented N from leaching from the soil, primarily by increasing populations of beneficial soil microbes. In contrast, tillage caused declines in populations of soil microbes, and should thus be minimized. Our results give growers the empirical data they need to decide whether or not to plant a cover crop.

4. Water use by grapevines is measured accurately by a novel dual heat pulse sap flow sensor. With impending limits on irrigation water in CA and other arid grape growing regions of the US, growers need to more accurately measure water use by grapevines, in order to irrigate more efficiently. ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA develop a novel sap flow sensor that is based on two existing heat pulse techniques. The sap flow sensor accurately detected changes in water use with various rates of irrigation and responded quickly to changes in water demand imposed by shading. With integration into real time irrigation systems, the sap flow sensor will help growers conserve irrigation water by applying the exact amount needed.

5. Proteins in grapevine roots, aquaporins, are markers of water uptake. Breeding programs are currently focusing on drought-tolerant grapevines, but there is no convenient means of assessing drought tolerance other than by growing the plants in the greenhouse and field, and evaluating their response to minimal irrigation. ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA examined levels of the proteins in grapevine roots that facilitate water movement (aquaporins), to determine if they respond consistently to known quantities of water and, thus, to evaluate aquaporin production as an indirect method of measuring drought tolerance. Aquaporin production was highest in drought-resistant rootstocks (1103P and 110R) and lowest in drought-susceptible rootstocks (420A and 101-14). Our research will advance breeding programs by accelerating the process of evaluating new grapevine varieties for drought-tolerance.

6. Cover crops have no effects on beneficial grapevine root microbes. There is a need to determine if cover crops can be used to enhance grapevine nutrition, specifically by increasing populations of beneficial arbuscular mycorrhizal fungi (AMF) that are critical for grapevine nutrition because they increase uptake of the nutrient phosphorus (P) from the soil. In a field trial, ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA examined grapevine AMF in the presence of two cover crop treatments (rye, triticale) that hosted some of the same AMF species as grapevines and, thus, were expected to increase populations of AMF in the vineyard. Despite the greater abundance of mycorrhizal plants in the vineyard with the cover crops, there were no increases in AMF in grapevine roots. This research suggests that planting cover crops that host the same AMF as grapevines is unlikely to increase AMF in grapevines.

7. Grapevine rootstocks host different soil microbial communities. Rootstocks have a significant effect on important characteristics of grape production (e.g., vigor, yield, fruit and wine quality, mineral nutrition, pathogen resistance, and drought tolerance), and differences in such characteristics among rootstocks may, in part, be attributable to differences in their soil microbial communities. In a field trial, ARS scientists in the Crops Pathology and Genetics Research Unit, in Davis, CA examined soil microbial communities among 10 different rootstocks, using DNA-based and culture-based methods. For the first time, we identified significant differences in the structural and functional diversity of the microbial community colonizing the different rootstocks, and this was found from microbes both within roots and on their surfaces. As many of the soil microbes are critical for nutrient cycling, their further characterization and association with specific nutrient pathways will allow growers to develop sustainable fertilization and irrigation programs with a better understanding of the biological component.

Review Publications
Baumgartner, K., Grubisha, L.C., Fujiyoshi, P.T., Garbelloto, M., Bergemann, S.E. 2009. Microsatellite markers for the diploid Basidiomycete fungus, Armillaria mellea. Molecular Ecology Resources. 9:943-946.

Baumgartner, K., Bergemann, S.E., Fujiyoshi, P.T., Rolshausen, P.E., Gubler, W.D. 2008. MICROSATELLITE MARKERS FOR THE GRAPEVINE PATHOGEN, EUTYPA LATA.. Molecular Ecology Resources. 9:222-224.



Steenwerth, K.L., Drenovsky, R.E., Lambert, J.J., Smart, D.R., Kluepfel, D.A., Scow, K.M. 2008. SOIL MORPHOLOGY, DEPTH AND GRAPEVINE ROOT FREQUENCY INFLUENCE MICROBIAL COMMUNITIES IN A PINOT NOIR VINEYARD. Soil Biology and Biochemistry. 40:1330-1340.

Last Modified: 2/23/2016
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